There was apparently a comic in the daily that showed Pope Benedict being against gay marriage (and distribution of condoms and some other things). Then, someone write an article saying that it was offensive (http://www.stanforddaily.com/2013/02/15/op-ed-the-irony-is-delicious).
Personally, I don't think that it's offensive to show someone defending their own opinions. Pope Benedict actually was against gay marriage. Someone who says that Pope Benedict is against gay marriage isn't being offensive; they're being factually accurate.
The article asserts that the Daily wouldn't publish a similar cartoon regarding Islam. I think that a key difference is context. The article says that the Daily wouldn't be okay with a cartoon of Allah or the Prophet Mohammad. Aside from religious issues regarding depiction, there's a difference between a historic religious figure and a current political and religious leader. I don't think, for instance, that it would be seen as offensive if someone were to show a cartoon of Mahmoud Ahmadinejad saying that there aren't gays in Iran or that the holocaust didn't happen (again, since he is a contemporary political figure who actually said those things).
The article also argues that, in an effort to create a safe and open space at Stanford, people will stamp out conservative ideas. Unlike the comic about Pope Benedict, I don't think that this is factually accurate. It might be that I'm not paying attention, but I can think of a few conservative Daily columnists over the years I've been here and many conservative op-ed writers (often complaining about how the Daily is liberal media), not to mention the Stanford Review. Not only that, but there are a ton of conservative events on campus, with the Pro Life crowd being more visible, in many ways, than the Pro Choice crowd, and with a very vocal group of Objectivists and economic conservatives.
I can't think of any instances of conservative ideas being "stamped out." I can think of many instances where people find those ideas offensive and say so, but I don't think that engaging in political debate counts as stamping out an idea. I can't think of anyone saying, "Well, I wanted to publish this conservative piece of writing, but the media on Stanford is too liberal, so they would stamp it out."
The author also suggests that when we feel offended, we should ask, "Am I upset because the comment or action was genuinely aimed at causing me physical or mental harm, or am I just mad because they don’t think like I do?" Here, I think that he is also on tenuous ground. In the legal case Brown v Board of Education, the Supreme Court found that separate was intrinsically unequal because, among other reasons, separate institutions made black kids feel inferior. The separate institutions may not have been aimed at causing mental harm, but they did cause harm nonetheless. Benign intent doesn't absolve an individual who causes harm. It seems like the author doesn't believe that gay people who love each other should be allowed to marry each other. I can imagine that advocates of separate and unequal institutions could make LGBTQ people feel bad and could cause them mental harm, and the high rates of suicide among LGBTQ people at least partially validates this idea. And on the note of physical harm, I think that "The Laramie Project" presents a compelling case for how that can happen.
That doesn't necessarily mean that everyone should have to say that people are equal. However, if I were to say that a certain class of people be denied rights that I enjoy, I wouldn't be surprised if they felt offended. It seems unreasonable to me that someone who publicly says that gay people who love each other shouldn't be able to marry each other would feel surprised if gay people felt offended.
So no, I don't feel mad that you don't think like I do. Most people don't think like I do on hundreds of issues. I am upset because, regardless of your intent, your words perpetuate a culture that causes large groups of people physical and mental harm.